HOMOLOGY BACKGROUND INFORMATION
Your goal is to determine relationships between proteins that define the cellular network. In
order to do this your group will analyze data obtained from homology searches.
Scientists are working to determine relationships between proteins by compiling all available
information about the genes and proteins in a network into a very large database. The gene
sequences for genomes of many organisms have been added to this database. A genome is an
organism’s entire sequence of DNA; therefore, if the DNA sequence is known, the proteins can
be predicted (recall DNA  mRNA  protein).
For many genes, functions and properties have been determined in the laboratory. But for many
other genes and proteins, scientists use this database to help them make hypotheses about the
functions and properties of these genes and proteins. Scientists compile what is known about the
genes and proteins in the network of interest. Then they analyze the information to hypothesize
relationships between the proteins. Information about genes with unknown functions can be
predicted by comparing their sequences to genes in the database that have known functions and
properties.
Searching for homologous genes, genes with similar sequences, is called homology
searching. Similar nucleotide sequences will result in proteins that have similar shapes and
folding patterns. Homologous proteins that are similar in their 3-dimensional shape will have
similar properties and functions. Homologous proteins are proteins that perform the same
function in two different organisms. For example, the hemoglobin protein that carries oxygen in
the blood of a cow is homologous to the hemoglobin protein in humans.
Information obtained from homology searching can help scientists determine if the protein
they are studying is an enzyme, a membrane-associated protein, or a transcription regulator.
Scientists can then study the protein’s role in the network more specifically. Scientists can also
determine what kind of regulatory sequences exist in the DNA that will affect the transcription of
the gene that codes for the protein. Ultimately, all this information helps scientists determine
how a protein interacts in a metabolic network.
HOMOLOGY SEARCH DATA
Gene
name
Protein
type
Description
"UAS" present
crtB1
enzyme
Substrate: GG-PP, Product: phytoene
Yes
crtY
enzyme
Substrate: lycopene, Product: beta-carotene
No
brp
enzyme
Substrate: beta-carotene, Product: retinal
Yes
bop
membraneassociated
Combines with retinal to form bacteriorhodopsin (bR), a
membrane protein that pumps H+ ions out of the cell using
energy from sunlight. The H+ ion concentration gradient is
used to produce ATP
Yes
bat
transcription
regulator
Binds DNA at sequences called "UAS" and increases
transcription by binding to RNA polymerase or related
transcription proteins.
Oxygen affects activity of bat.
Light affects activity of bat.
Yes
Gene name:
Gene names are often written in italics; the protein coded by the gene is often written in regular font.
For example, crtB1is the gene that codes for the crtB1 protein.
Protein type:
Enzymes convert specific substrates into products; membrane-associated proteins are found near
or in the cell membrane; and transcription regulators are proteins that control the amount of mRNA
transcription by binding to RNA polymerase and regions of DNA in particular genes.
Description:
Information about known functions for each of the proteins. For enzymes, S: means substrate and
P: means product.
“UAS” regulatory sequence in promoter:
Some genes have activator sequences in their promoters called “Upstream Activator Sequences”.
Transcription regulator proteins (see bat) bind to the UAS and RNA polymerase to increase the
amount of mRNA transcription. Simply speaking, bind the UAS and there will be an increase in the
product of that gene.
ANALYSIS:
1. Fill in the spaces below using the information provided on the Homology Data Table. Fill in the
gene name (protein) that catalyzes each reaction.
lycopene
Protein
A
T
P
GG-PP
beta-carotene
phytoene
Protein
Protein
retinal
phytoene
brpProtein
bacteriorhodopsin
2. What is the result of the UAS being bound?
3. In the production of bacteriorhodopsin which protein binds to UAS?
4. If the transcription regulator is bound to the UAS on the DNA, which genes will have their
products increase (see table)?
5. In the presence of light, bat production will increase. Knowing this, how does light effect the
pathway of bacteriorhodopsin production?
Use the diagram above to help explain the steps involved.
KEY FOR HOMOLOGY DATA
Directions: Fill in the gene name (protein) that catalyzes each reaction using the information
provided on the Homology Data Table. Your goal is to determine how light affects the amount of
bacteriorhodopsin in the halo cell.
lycopene
P
r
crtY
o
Protein
t
e
beta-carotene
i
n
GG-PP
crtB1
ProteinProtein
Bop
retinal
ATP
Protein
bacteriorhodopsin
1. How does the amount of light affect the amount of bacteriorhodopsin in halo?
Increase light = increase bacteriorhodopsin
2. Using your data table as a guide, which protein is likely the sensor that detects the presence of
light and oxygen? What specific information suggests this?
bat-- Binds DNA at sequences called "UAS" and increases transcription by binding to RNA
polymerase or related transcription proteins.
Oxygen = more likely to bind at UAS = more transcription
Oxygen affects bat’s ability to bind UAS
Light affects bat’s ability to bind UAS.
3. What does UAS mean? Which genes have a UAS? How does having a UAS affect the amount
of transcription of the genes?
“UAS” regulatory sequence in promoter:
Some genes have activator sequences in their promoters called “Upstream Activator Sequences”.
Transcription regulator proteins bind to the UAS and RNA polymerase to increase the amount of
mRNA transcription.
4. Which protein binds to the UAS?
bat
5. Thinking of your responses to the above questions, suggest a hypothesis for how the network is
regulated in response to light and oxygen. You can explain your hypothesis with a diagram in
addition to words.
Responses will vary
6. What data/information would help you test the hypotheses or support or refute the hypothesis
you suggested in question #5?
How the biochemistry is involved; what happens if a piece is missing (gene expression).